I managed to load TiO.struct and set the vibrations for the Ti, and it
is there for all equivalent sites so this works fine. (The button at
the top is fine; the right-mouse click does not show vibrations as an
option.)
However, I could not find a way to alter the number of unit cells
being shown without reloading the structure; is there a way of doing
this?
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
N.B., does a "jmolscript:" get embedded in a { } (i.e. C)?
On 5/21/09, Robert Hanson <[email protected]> wrote:
> The Jmol application probably does have some minor issues there. I'm not
> sure if you load vibrational data by script, for example, that the vibration
> button works. Most of us use the console. But should that be the case, then
> a bug report should be filed so I can get to it.
>
> If you have implemented vibrations in an XYZ file, then that's all you need.
> Just write a little Jmol script that
>
> 1) loads the Wien2k or other file with full symmetry
> 2) reads that xyz file into a variable using vibdata = file("yyy.xyz")
> 3) changes that to Jmol script format and runs it.
>
>
> I think this is a few lines of Jmol script:
>
> function applyVibData(filename)
> var vibdata = load(filename)
> var S = vibdata.split()
> var myscript = ""
> for (var i = 3; i <= S.size; i=i+1)
> var line = S[i]
> # change the numbers below to match your file format -- I'm guessing
> here
> var x = "{" + (S[i])[3][45] + "}"
> var v = "{" + (S[i])[48][0] + "}"
> myscript = myscript + "x=" + x + ";v=" + v+";{within(-2.5,x)}.vxyz =
> v\n"
> end for
> script inline @myscript
> end function
>
>
>
> Bob
>
>
>
> On Thu, May 21, 2009 at 7:11 AM, Laurence Marks <[email protected]>
> wrote:
> >
> > Let me be a bit more specific. I have implemented vibrations using an
> > xyz file, but since this does not contain the crystal lattice
> > information cell repeats have to be done ahead of time. What I would
> > like to do is for a crystal (cif, Wien2k, other) add vibrations
> > (probably with a script) and then display these using "standard" tools
> > for repeating the unit cell etc, with the vibrations obeying the
> > appropriate symmetry and translational operations.
> >
> > When I attempted to do this it looked like this is not currently
> > supported (the vibrations button was inactive) although I might not
> > have done it correctly and I don't think I used the console.
> >
> > N.B., there are some issues with the vibrations having a lower
> > symmetry than the unit cell so strictly speaking the cell should have
> > P1 symmetry. Walk before run; are vibrations active for crystals.
> >
> > N.N.B., an alternative would be to be able to add crystalline repeat
> > information to an xyz format.
> >
> > --
> > Laurence Marks
> > Department of Materials Science and Engineering
> > MSE Rm 2036 Cook Hall
> > 2220 N Campus Drive
> > Northwestern University
> > Evanston, IL 60208, USA
> > Tel: (847) 491-3996 Fax: (847) 491-7820
> > email: L-marks at northwestern dot edu
> > Web: www.numis.northwestern.edu
> > Chair, Commission on Electron Crystallography of IUCR
> > www.numis.northwestern.edu/
> > Electron crystallography is the branch of science that uses electron
> > scattering to study the structure of matter.
> >
> >
> ------------------------------------------------------------------------------
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> >
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> ------------------------------------------------------------------------------
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> is a gathering of tech-side developers & brand creativity professionals.
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>
>
--
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
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iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
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